0s autopkgtest [17:33:48]: starting date and time: 2025-10-18 17:33:48+0000 0s autopkgtest [17:33:48]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [17:33:48]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hgea46wv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade coot --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-2.secgroup --name adt-resolute-amd64-coot-20251018-173348-juju-7f2275-prod-proposed-migration-environment-15-ba6a6c66-e53d-46c2-a43b-fb5f7e2dcdf3 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-coot-20251018-173348-juju-7f2275-prod-proposed-migration-environment-15-ba6a6c66-e53d-46c2-a43b-fb5f7e2dcdf3 from image adt/ubuntu-resolute-amd64-server-20251018.img (UUID 1e43d7d4-3f39-4b59-975d-5a285d0b86c1)... 56s autopkgtest [17:34:44]: testbed dpkg architecture: amd64 56s autopkgtest [17:34:44]: testbed apt version: 3.1.6ubuntu2 56s autopkgtest [17:34:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 56s autopkgtest [17:34:44]: testbed release detected to be: None 57s autopkgtest [17:34:45]: updating testbed package index (apt update) 57s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 58s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 58s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 58s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 58s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 58s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 58s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 58s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 58s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [46.6 kB] 58s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [85.2 kB] 58s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 58s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 58s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [87.6 kB] 58s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [233 kB] 58s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [8376 B] 58s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [2772 B] 58s Fetched 972 kB in 1s (929 kB/s) 59s Reading package lists... 60s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 60s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 61s Reading package lists... 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Calculating upgrade... 62s The following packages will be upgraded: 62s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 62s libpython3-stdlib lto-disabled-list python3 python3-minimal 62s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s Need to get 2763 kB of archives. 62s After this operation, 2048 B of additional disk space will be used. 62s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.7-2 [27.8 kB] 62s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.7-2 [23.9 kB] 62s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.7-2 [10.6 kB] 62s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.8ubuntu1 [1140 kB] 62s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.8ubuntu1 [1438 kB] 63s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-1.0-1 amd64 1.86.0-6 [85.9 kB] 63s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-2.0 amd64 1.86.0-6 [25.3 kB] 63s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 lto-disabled-list all 71 [12.5 kB] 63s dpkg-preconfigure: unable to re-open stdin: No such file or directory 63s Fetched 2763 kB in 1s (2694 kB/s) 63s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78439 files and directories currently installed.) 63s Preparing to unpack .../python3-minimal_3.13.7-2_amd64.deb ... 63s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 63s Setting up python3-minimal (3.13.7-2) ... 63s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78439 files and directories currently installed.) 63s Preparing to unpack .../0-python3_3.13.7-2_amd64.deb ... 63s running python pre-rtupdate hooks for python3.13... 63s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 63s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_amd64.deb ... 63s Unpacking libpython3-stdlib:amd64 (3.13.7-2) over (3.13.7-1) ... 63s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_amd64.deb ... 63s Unpacking libapt-pkg7.0:amd64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 64s Preparing to unpack .../3-apt_3.1.8ubuntu1_amd64.deb ... 64s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 64s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_amd64.deb ... 64s Unpacking libgirepository-1.0-1:amd64 (1.86.0-6) over (1.84.0-1) ... 64s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_amd64.deb ... 64s Unpacking gir1.2-girepository-2.0:amd64 (1.86.0-6) over (1.84.0-1) ... 64s Preparing to unpack .../6-lto-disabled-list_71_all.deb ... 64s Unpacking lto-disabled-list (71) over (69) ... 64s Setting up lto-disabled-list (71) ... 64s Setting up libgirepository-1.0-1:amd64 (1.86.0-6) ... 64s Setting up libapt-pkg7.0:amd64 (3.1.8ubuntu1) ... 64s Setting up libpython3-stdlib:amd64 (3.13.7-2) ... 64s Setting up apt (3.1.8ubuntu1) ... 64s Setting up python3 (3.13.7-2) ... 64s running python rtupdate hooks for python3.13... 64s running python post-rtupdate hooks for python3.13... 64s Setting up gir1.2-girepository-2.0:amd64 (1.86.0-6) ... 64s Processing triggers for man-db (2.13.1-1) ... 66s Processing triggers for libc-bin (2.42-0ubuntu3) ... 66s autopkgtest [17:34:54]: upgrading testbed (apt dist-upgrade and autopurge) 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Calculating upgrade... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Solving dependencies... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s autopkgtest [17:34:56]: rebooting testbed after setup commands that affected boot 87s autopkgtest [17:35:15]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 90s autopkgtest [17:35:18]: @@@@@@@@@@@@@@@@@@@@ apt-source coot 98s Get:1 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.15+dfsg-1build1 (dsc) [2996 B] 98s Get:2 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.15+dfsg-1build1 (tar) [89.2 MB] 98s Get:3 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.15+dfsg-1build1 (diff) [53.7 kB] 99s gpgv: Signature made Fri Aug 8 03:34:32 2025 UTC 99s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 99s gpgv: Can't check signature: No public key 99s dpkg-source: warning: cannot verify inline signature for ./coot_1.1.15+dfsg-1build1.dsc: no acceptable signature found 100s autopkgtest [17:35:28]: testing package coot version 1.1.15+dfsg-1build1 101s autopkgtest [17:35:29]: build not needed 109s autopkgtest [17:35:37]: test command1: preparing testbed 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Solving dependencies... 110s The following NEW packages will be installed: 110s adwaita-icon-theme coot coot-data coot-doc dconf-gsettings-backend 110s dconf-service fontconfig fontconfig-config fonts-freefont-ttf 110s fonts-noto-core fonts-noto-mono gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 110s gir1.2-graphene-1.0 gir1.2-gtk-4.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 110s gtk-update-icon-cache hicolor-icon-theme libamd-comgr2 libamdhip64-5 110s libasound2-data libasound2t64 libblas3 libboost-iostreams1.83.0 110s libboost-iostreams1.88.0 libboost-numpy1.83.0 libboost-python1.83.0 110s libboost-python1.88.0 libboost-serialization1.83.0 110s libboost-serialization1.88.0 libcairo-gobject2 libcairo-script-interpreter2 110s libcairo2 libccp4-data libccp4c0t64 libclipper2 libcoordgen3 libcootapi-dev 110s libcootapi1.1 libcpdb-frontend2t64 libcpdb2t64 libdatrie1 libdconf1 110s libdeflate0 libdrm-amdgpu1 libdrm-intel1 libegl-mesa0 libegl1 libepoxy0 110s libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfontconfig1 110s libgbm1 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1 110s libgl1-mesa-dri libgles2 libglvnd0 libglx-mesa0 libglx0 libgomp1 110s libgraphene-1.0-0 libgraphite2-3 libgsl28 libgslcblas0 libgstreamer-gl1.0-0 110s libgstreamer-plugins-base1.0-0 libgstreamer1.0-0 libgtk-4-1 libgtk-4-common 110s libgudev-1.0-0 libharfbuzz-gobject0 libharfbuzz-subset0 libharfbuzz0b 110s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 110s libibumad3 libinchi1.07 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 110s libllvm17t64 liblzo2-2 libmaeparser1 libmmdb2-0 libogg0 libopenmpi40 110s liborc-0.4-0t64 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 110s libpangoxft-1.0-0 libpciaccess0 libpixman-1-0 libpsm2-2 librdkit1t64 110s librdmacm1t64 librsvg2-2 libsharpyuv0 libssm2 libthai-data libthai0 libtiff6 110s libucx0 libvorbis0a libvorbisfile3 libvulkan1 libwayland-client0 110s libwayland-cursor0 libwayland-egl1 libwebp7 libx11-xcb1 libxcb-dri3-0 110s libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 110s libxcb-sync1 libxcb-xfixes0 libxcursor1 libxdamage1 libxfixes3 libxft2 110s libxi6 libxinerama1 libxnvctrl0 libxrandr2 libxrender1 libxshmfence1 110s libxxf86vm1 libze1 mesa-libgallium ocl-icd-libopencl1 python3-numpy 110s python3-numpy-dev python3-rdkit rdkit-data refmac-dictionary sfftw2 110s ttf-bitstream-vera 110s 0 upgraded, 150 newly installed, 0 to remove and 0 not upgraded. 110s Need to get 188 MB of archives. 110s After this operation, 908 MB of additional disk space will be used. 110s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 110s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 110s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 111s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 112s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 113s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-5 [8326 B] 113s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 113s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 113s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 113s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 113s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 113s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 113s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 113s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 113s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-5 [157 kB] 113s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 gtk-update-icon-cache amd64 4.20.1+ds-2 [54.6 kB] 113s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB] 113s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 adwaita-icon-theme all 49.0-1 [581 kB] 113s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-noto-mono all 20201225-2 [435 kB] 113s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-noto-core all 20201225-2 [13.3 MB] 114s Get:21 http://ftpmaster.internal/ubuntu resolute/universe amd64 ttf-bitstream-vera all 1.10-8.2 [244 kB] 114s Get:22 http://ftpmaster.internal/ubuntu resolute/universe amd64 coot-data all 1.1.15+dfsg-1build1 [11.9 MB] 115s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB] 115s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 115s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 115s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 115s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 115s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 115s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 115s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 115s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo-gobject2 amd64 1.18.4-1build1 [128 kB] 115s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-freedesktop amd64 1.86.0-6 [65.9 kB] 115s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-gdkpixbuf-2.0 amd64 2.42.12+dfsg-5 [9284 B] 115s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphene-1.0-0 amd64 1.10.8-5 [46.0 kB] 115s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-graphene-1.0 amd64 1.10.8-5 [11.1 kB] 115s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 115s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 115s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz-gobject0 amd64 10.2.0-1 [34.6 kB] 115s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-harfbuzz-0.0 amd64 10.2.0-1 [45.1 kB] 115s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.15.0-2.3ubuntu1 [180 kB] 115s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 115s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.13-4 [19.3 kB] 115s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 115s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.56.3-1build1 [247 kB] 115s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1build1 [55.0 kB] 115s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1build1 [30.3 kB] 115s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 115s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoxft-1.0-0 amd64 1.56.3-1build1 [21.4 kB] 115s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-pango-1.0 amd64 1.56.3-1build1 [34.6 kB] 115s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzo2-2 amd64 2.10-3build1 [57.5 kB] 115s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo-script-interpreter2 amd64 1.18.4-1build1 [65.0 kB] 115s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libcpdb2t64 amd64 2.0~b7-0ubuntu3 [31.8 kB] 115s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libcpdb-frontend2t64 amd64 2.0~b7-0ubuntu3 [21.5 kB] 115s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB] 115s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libglvnd0 amd64 1.7.0-1build2 [65.1 kB] 115s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.125-1 [21.6 kB] 115s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libpciaccess0 amd64 0.18.1-1ubuntu2 [19.0 kB] 115s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-intel1 amd64 2.4.125-1 [64.9 kB] 115s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libx11-xcb1 amd64 2:1.8.12-1build1 [8044 B] 115s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-dri3-0 amd64 1.17.0-2build1 [8036 B] 115s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-present0 amd64 1.17.0-2build1 [6446 B] 115s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-randr0 amd64 1.17.0-2build1 [19.7 kB] 115s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-sync1 amd64 1.17.0-2build1 [10.1 kB] 115s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-xfixes0 amd64 1.17.0-2build1 [11.1 kB] 115s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libxshmfence1 amd64 1.3.3-1 [5262 B] 115s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 mesa-libgallium amd64 25.2.3-1ubuntu1 [11.1 MB] 116s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libgbm1 amd64 25.2.3-1ubuntu1 [34.0 kB] 116s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-client0 amd64 1.24.0-1build1 [29.6 kB] 116s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libegl-mesa0 amd64 25.2.3-1ubuntu1 [117 kB] 116s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libegl1 amd64 1.7.0-1build2 [31.2 kB] 116s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-glx0 amd64 1.17.0-2build1 [27.6 kB] 116s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B] 116s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libvulkan1 amd64 1.4.321.0-1 [154 kB] 116s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgl1-mesa-dri amd64 25.2.3-1ubuntu1 [36.9 kB] 116s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libglx-mesa0 amd64 25.2.3-1ubuntu1 [110 kB] 116s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libglx0 amd64 1.7.0-1build2 [40.3 kB] 116s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libgl1 amd64 1.7.0-1build2 [101 kB] 116s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libgstreamer1.0-0 amd64 1.26.6-1 [1204 kB] 116s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 liborc-0.4-0t64 amd64 1:0.4.41-1 [252 kB] 116s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libgstreamer-plugins-base1.0-0 amd64 1.26.6-1 [905 kB] 116s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7 [16.9 kB] 116s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-cursor0 amd64 1.24.0-1build1 [11.1 kB] 116s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-egl1 amd64 1.24.0-1build1 [6474 B] 116s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 libgstreamer-gl1.0-0 amd64 1.26.6-1 [227 kB] 116s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz-subset0 amd64 10.2.0-1 [553 kB] 116s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 librsvg2-2 amd64 2.60.0+dfsg-1build1 [1829 kB] 116s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB] 116s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcursor1 amd64 1:1.2.3-1 [23.1 kB] 116s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B] 116s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 116s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B] 116s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB] 116s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 libgles2 amd64 1.7.0-1build2 [17.5 kB] 116s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 libdconf1 amd64 0.40.0-5willsync1 [41.3 kB] 116s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 dconf-service amd64 0.40.0-5willsync1 [28.7 kB] 116s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 dconf-gsettings-backend amd64 0.40.0-5willsync1 [23.5 kB] 116s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 libgtk-4-common all 4.20.1+ds-2 [1528 kB] 116s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 libgtk-4-1 amd64 4.20.1+ds-2 [3411 kB] 116s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-gtk-4.0 amd64 4.20.1+ds-2 [220 kB] 116s Get:100 http://ftpmaster.internal/ubuntu resolute/universe amd64 rdkit-data all 202503.1-4 [12.6 MB] 117s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-python1.83.0 amd64 1.83.0-5ubuntu1 [320 kB] 117s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 libboost-numpy1.83.0 amd64 1.83.0-5ubuntu1 [245 kB] 117s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 libboost-serialization1.83.0 amd64 1.83.0-5ubuntu1 [354 kB] 117s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcoordgen3 amd64 3.0.2-1 [215 kB] 117s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-5ubuntu1 [263 kB] 117s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 libinchi1.07 amd64 1.07.3+dfsg-1 [702 kB] 117s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-iostreams1.88.0 amd64 1.88.0-1.4ubuntu1 [264 kB] 117s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmaeparser1 amd64 1.3.1-1build3 [93.9 kB] 117s Get:109 http://ftpmaster.internal/ubuntu resolute/universe amd64 librdkit1t64 amd64 202503.1-4 [5801 kB] 118s Get:110 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rdkit amd64 202503.1-4 [4820 kB] 118s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 refmac-dictionary all 5.41-3 [16.7 MB] 118s Get:112 http://ftpmaster.internal/ubuntu resolute/main amd64 libasound2-data all 1.2.14-1ubuntu1 [21.2 kB] 118s Get:113 http://ftpmaster.internal/ubuntu resolute/main amd64 libasound2t64 amd64 1.2.14-1ubuntu1 [407 kB] 118s Get:114 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-python1.88.0 amd64 1.88.0-1.4ubuntu1 [323 kB] 118s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 libboost-serialization1.88.0 amd64 1.88.0-1.4ubuntu1 [356 kB] 119s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 libccp4-data all 8.0.0-5 [65.2 kB] 119s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 libccp4c0t64 amd64 8.0.0-5 [100 kB] 119s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmmdb2-0 amd64 2.0.22-1 [363 kB] 119s Get:119 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build1 [98.8 kB] 119s Get:120 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10build1 [8360 B] 119s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 119s Get:122 http://ftpmaster.internal/ubuntu resolute/main amd64 librdmacm1t64 amd64 56.1-1ubuntu1 [71.4 kB] 119s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfabric1 amd64 2.1.0-1.1 [697 kB] 119s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhwloc15 amd64 2.12.2-1 [181 kB] 119s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 libllvm17t64 amd64 1:17.0.6-22build1 [25.9 MB] 119s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build3 [14.3 MB] 120s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhsakmt1 amd64 6.2.4+ds-1 [66.8 kB] 120s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhsa-runtime64-1 amd64 6.1.2-3 [564 kB] 120s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamdhip64-5 amd64 5.7.1-6 [9698 kB] 120s Get:130 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-5ubuntu1 [151 kB] 120s Get:131 http://ftpmaster.internal/ubuntu resolute/main amd64 libibumad3 amd64 56.1-1ubuntu1 [31.3 kB] 120s Get:132 http://ftpmaster.internal/ubuntu resolute/main amd64 libibmad5 amd64 56.1-1ubuntu1 [44.0 kB] 120s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 libucx0 amd64 1.19.0+ds-1 [1308 kB] 120s Get:134 http://ftpmaster.internal/ubuntu resolute/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 120s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 libze1 amd64 1.24.1-2 [599 kB] 120s Get:136 http://ftpmaster.internal/ubuntu resolute/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [41.0 kB] 120s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhwloc-plugins amd64 2.12.2-1 [22.2 kB] 120s Get:138 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenmpi40 amd64 5.0.8-8ubuntu1 [3384 kB] 120s Get:139 http://ftpmaster.internal/ubuntu resolute/universe amd64 sfftw2 amd64 2.1.5-7build1 [224 kB] 120s Get:140 http://ftpmaster.internal/ubuntu resolute/universe amd64 libclipper2 amd64 2.1.20201109-2build1 [1188 kB] 120s Get:141 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgslcblas0 amd64 2.8+dfsg-5.1ubuntu1 [133 kB] 120s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgsl28 amd64 2.8+dfsg-5.1ubuntu1 [1104 kB] 120s Get:143 http://ftpmaster.internal/ubuntu resolute/universe amd64 libssm2 amd64 1.4.0-2build1 [87.7 kB] 120s Get:144 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcootapi1.1 amd64 1.1.15+dfsg-1build1 [4013 kB] 120s Get:145 http://ftpmaster.internal/ubuntu resolute/main amd64 libogg0 amd64 1.3.5-3build1 [22.7 kB] 120s Get:146 http://ftpmaster.internal/ubuntu resolute/main amd64 libvorbis0a amd64 1.3.7-3build1 [103 kB] 120s Get:147 http://ftpmaster.internal/ubuntu resolute/main amd64 libvorbisfile3 amd64 1.3.7-3build1 [18.0 kB] 120s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 coot amd64 1.1.15+dfsg-1build1 [8889 kB] 121s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 coot-doc all 1.1.15+dfsg-1build1 [2048 kB] 121s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcootapi-dev amd64 1.1.15+dfsg-1build1 [25.5 kB] 121s Fetched 188 MB in 11s (17.2 MB/s) 121s Selecting previously unselected package python3-numpy-dev:amd64. 121s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78439 files and directories currently installed.) 121s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 121s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 121s Selecting previously unselected package libblas3:amd64. 121s Preparing to unpack .../001-libblas3_3.12.1-6build1_amd64.deb ... 121s Unpacking libblas3:amd64 (3.12.1-6build1) ... 121s Selecting previously unselected package libgfortran5:amd64. 121s Preparing to unpack .../002-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 121s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 121s Selecting previously unselected package liblapack3:amd64. 121s Preparing to unpack .../003-liblapack3_3.12.1-6build1_amd64.deb ... 121s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 121s Selecting previously unselected package python3-numpy. 121s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 121s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 121s Selecting previously unselected package libgdk-pixbuf2.0-common. 121s Preparing to unpack .../005-libgdk-pixbuf2.0-common_2.42.12+dfsg-5_all.deb ... 121s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-5) ... 121s Selecting previously unselected package libjpeg-turbo8:amd64. 121s Preparing to unpack .../006-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 121s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 121s Selecting previously unselected package libjpeg8:amd64. 121s Preparing to unpack .../007-libjpeg8_8c-2ubuntu11_amd64.deb ... 121s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 121s Selecting previously unselected package libdeflate0:amd64. 121s Preparing to unpack .../008-libdeflate0_1.23-2_amd64.deb ... 121s Unpacking libdeflate0:amd64 (1.23-2) ... 122s Selecting previously unselected package libjbig0:amd64. 122s Preparing to unpack .../009-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 122s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 122s Selecting previously unselected package liblerc4:amd64. 122s Preparing to unpack .../010-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 122s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 122s Selecting previously unselected package libsharpyuv0:amd64. 122s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1_amd64.deb ... 122s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 122s Selecting previously unselected package libwebp7:amd64. 122s Preparing to unpack .../012-libwebp7_1.5.0-0.1_amd64.deb ... 122s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 122s Selecting previously unselected package libtiff6:amd64. 122s Preparing to unpack .../013-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 122s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 122s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 122s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.42.12+dfsg-5_amd64.deb ... 122s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-5) ... 122s Selecting previously unselected package gtk-update-icon-cache. 122s Preparing to unpack .../015-gtk-update-icon-cache_4.20.1+ds-2_amd64.deb ... 122s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 122s No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. 122s Unpacking gtk-update-icon-cache (4.20.1+ds-2) ... 122s Selecting previously unselected package hicolor-icon-theme. 122s Preparing to unpack .../016-hicolor-icon-theme_0.18-2_all.deb ... 122s Unpacking hicolor-icon-theme (0.18-2) ... 122s Selecting previously unselected package adwaita-icon-theme. 122s Preparing to unpack .../017-adwaita-icon-theme_49.0-1_all.deb ... 122s Unpacking adwaita-icon-theme (49.0-1) ... 122s Selecting previously unselected package fonts-noto-mono. 122s Preparing to unpack .../018-fonts-noto-mono_20201225-2_all.deb ... 122s Unpacking fonts-noto-mono (20201225-2) ... 122s Selecting previously unselected package fonts-noto-core. 122s Preparing to unpack .../019-fonts-noto-core_20201225-2_all.deb ... 122s Unpacking fonts-noto-core (20201225-2) ... 122s Selecting previously unselected package ttf-bitstream-vera. 122s Preparing to unpack .../020-ttf-bitstream-vera_1.10-8.2_all.deb ... 122s Unpacking ttf-bitstream-vera (1.10-8.2) ... 122s Selecting previously unselected package coot-data. 122s Preparing to unpack .../021-coot-data_1.1.15+dfsg-1build1_all.deb ... 122s Unpacking coot-data (1.1.15+dfsg-1build1) ... 122s Selecting previously unselected package fonts-freefont-ttf. 122s Preparing to unpack .../022-fonts-freefont-ttf_20211204+svn4273-2_all.deb ... 122s Unpacking fonts-freefont-ttf (20211204+svn4273-2) ... 122s Selecting previously unselected package fontconfig-config. 122s Preparing to unpack .../023-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 123s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 123s Selecting previously unselected package libfontconfig1:amd64. 123s Preparing to unpack .../024-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 123s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 123s Selecting previously unselected package libpixman-1-0:amd64. 123s Preparing to unpack .../025-libpixman-1-0_0.44.0-3_amd64.deb ... 123s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 123s Selecting previously unselected package libxcb-render0:amd64. 123s Preparing to unpack .../026-libxcb-render0_1.17.0-2build1_amd64.deb ... 123s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 123s Selecting previously unselected package libxcb-shm0:amd64. 123s Preparing to unpack .../027-libxcb-shm0_1.17.0-2build1_amd64.deb ... 123s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 123s Selecting previously unselected package libxrender1:amd64. 123s Preparing to unpack .../028-libxrender1_1%3a0.9.12-1_amd64.deb ... 123s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 123s Selecting previously unselected package libcairo2:amd64. 123s Preparing to unpack .../029-libcairo2_1.18.4-1build1_amd64.deb ... 123s Unpacking libcairo2:amd64 (1.18.4-1build1) ... 123s Selecting previously unselected package libcairo-gobject2:amd64. 123s Preparing to unpack .../030-libcairo-gobject2_1.18.4-1build1_amd64.deb ... 123s Unpacking libcairo-gobject2:amd64 (1.18.4-1build1) ... 123s Selecting previously unselected package gir1.2-freedesktop:amd64. 123s Preparing to unpack .../031-gir1.2-freedesktop_1.86.0-6_amd64.deb ... 123s Unpacking gir1.2-freedesktop:amd64 (1.86.0-6) ... 123s Selecting previously unselected package gir1.2-gdkpixbuf-2.0:amd64. 123s Preparing to unpack .../032-gir1.2-gdkpixbuf-2.0_2.42.12+dfsg-5_amd64.deb ... 123s Unpacking gir1.2-gdkpixbuf-2.0:amd64 (2.42.12+dfsg-5) ... 123s Selecting previously unselected package libgraphene-1.0-0:amd64. 123s Preparing to unpack .../033-libgraphene-1.0-0_1.10.8-5_amd64.deb ... 123s Unpacking libgraphene-1.0-0:amd64 (1.10.8-5) ... 123s Selecting previously unselected package gir1.2-graphene-1.0:amd64. 123s Preparing to unpack .../034-gir1.2-graphene-1.0_1.10.8-5_amd64.deb ... 123s Unpacking gir1.2-graphene-1.0:amd64 (1.10.8-5) ... 123s Selecting previously unselected package libgraphite2-3:amd64. 123s Preparing to unpack .../035-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 123s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 123s Selecting previously unselected package libharfbuzz0b:amd64. 123s Preparing to unpack .../036-libharfbuzz0b_10.2.0-1_amd64.deb ... 123s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 123s Selecting previously unselected package libharfbuzz-gobject0:amd64. 123s Preparing to unpack .../037-libharfbuzz-gobject0_10.2.0-1_amd64.deb ... 123s Unpacking libharfbuzz-gobject0:amd64 (10.2.0-1) ... 123s Selecting previously unselected package gir1.2-harfbuzz-0.0:amd64. 123s Preparing to unpack .../038-gir1.2-harfbuzz-0.0_10.2.0-1_amd64.deb ... 123s Unpacking gir1.2-harfbuzz-0.0:amd64 (10.2.0-1) ... 123s Selecting previously unselected package fontconfig. 123s Preparing to unpack .../039-fontconfig_2.15.0-2.3ubuntu1_amd64.deb ... 123s Unpacking fontconfig (2.15.0-2.3ubuntu1) ... 123s Selecting previously unselected package libthai-data. 123s Preparing to unpack .../040-libthai-data_0.1.29-2build1_all.deb ... 123s Unpacking libthai-data (0.1.29-2build1) ... 123s Selecting previously unselected package libdatrie1:amd64. 123s Preparing to unpack .../041-libdatrie1_0.2.13-4_amd64.deb ... 123s Unpacking libdatrie1:amd64 (0.2.13-4) ... 123s Selecting previously unselected package libthai0:amd64. 123s Preparing to unpack .../042-libthai0_0.1.29-2build1_amd64.deb ... 123s Unpacking libthai0:amd64 (0.1.29-2build1) ... 123s Selecting previously unselected package libpango-1.0-0:amd64. 123s Preparing to unpack .../043-libpango-1.0-0_1.56.3-1build1_amd64.deb ... 123s Unpacking libpango-1.0-0:amd64 (1.56.3-1build1) ... 123s Selecting previously unselected package libpangoft2-1.0-0:amd64. 123s Preparing to unpack .../044-libpangoft2-1.0-0_1.56.3-1build1_amd64.deb ... 123s Unpacking libpangoft2-1.0-0:amd64 (1.56.3-1build1) ... 123s Selecting previously unselected package libpangocairo-1.0-0:amd64. 123s Preparing to unpack .../045-libpangocairo-1.0-0_1.56.3-1build1_amd64.deb ... 123s Unpacking libpangocairo-1.0-0:amd64 (1.56.3-1build1) ... 123s Selecting previously unselected package libxft2:amd64. 123s Preparing to unpack .../046-libxft2_2.3.6-1build1_amd64.deb ... 123s Unpacking libxft2:amd64 (2.3.6-1build1) ... 123s 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unselected package libvulkan1:amd64. 124s Preparing to unpack .../072-libvulkan1_1.4.321.0-1_amd64.deb ... 124s Unpacking libvulkan1:amd64 (1.4.321.0-1) ... 124s Selecting previously unselected package libgl1-mesa-dri:amd64. 124s Preparing to unpack .../073-libgl1-mesa-dri_25.2.3-1ubuntu1_amd64.deb ... 124s Unpacking libgl1-mesa-dri:amd64 (25.2.3-1ubuntu1) ... 124s Selecting previously unselected package libglx-mesa0:amd64. 124s Preparing to unpack .../074-libglx-mesa0_25.2.3-1ubuntu1_amd64.deb ... 124s Unpacking libglx-mesa0:amd64 (25.2.3-1ubuntu1) ... 124s Selecting previously unselected package libglx0:amd64. 124s Preparing to unpack .../075-libglx0_1.7.0-1build2_amd64.deb ... 124s Unpacking libglx0:amd64 (1.7.0-1build2) ... 124s Selecting previously unselected package libgl1:amd64. 124s Preparing to unpack .../076-libgl1_1.7.0-1build2_amd64.deb ... 124s Unpacking libgl1:amd64 (1.7.0-1build2) ... 124s Selecting previously unselected package libgstreamer1.0-0:amd64. 124s Preparing to unpack .../077-libgstreamer1.0-0_1.26.6-1_amd64.deb ... 124s Unpacking libgstreamer1.0-0:amd64 (1.26.6-1) ... 124s Selecting previously unselected package liborc-0.4-0t64:amd64. 124s Preparing to unpack .../078-liborc-0.4-0t64_1%3a0.4.41-1_amd64.deb ... 124s Unpacking liborc-0.4-0t64:amd64 (1:0.4.41-1) ... 124s Selecting previously unselected package libgstreamer-plugins-base1.0-0:amd64. 124s Preparing to unpack .../079-libgstreamer-plugins-base1.0-0_1.26.6-1_amd64.deb ... 124s Unpacking libgstreamer-plugins-base1.0-0:amd64 (1.26.6-1) ... 124s Selecting previously unselected package libgudev-1.0-0:amd64. 124s Preparing to unpack .../080-libgudev-1.0-0_1%3a238-7_amd64.deb ... 124s Unpacking libgudev-1.0-0:amd64 (1:238-7) ... 124s Selecting previously unselected package libwayland-cursor0:amd64. 124s Preparing to unpack .../081-libwayland-cursor0_1.24.0-1build1_amd64.deb ... 124s Unpacking libwayland-cursor0:amd64 (1.24.0-1build1) ... 124s Selecting previously unselected package 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package libxcursor1:amd64. 124s Preparing to unpack .../087-libxcursor1_1%3a1.2.3-1_amd64.deb ... 124s Unpacking libxcursor1:amd64 (1:1.2.3-1) ... 124s Selecting previously unselected package libxdamage1:amd64. 124s Preparing to unpack .../088-libxdamage1_1%3a1.1.6-1build1_amd64.deb ... 124s Unpacking libxdamage1:amd64 (1:1.1.6-1build1) ... 124s Selecting previously unselected package libxi6:amd64. 124s Preparing to unpack .../089-libxi6_2%3a1.8.2-1_amd64.deb ... 124s Unpacking libxi6:amd64 (2:1.8.2-1) ... 124s Selecting previously unselected package libxinerama1:amd64. 124s Preparing to unpack .../090-libxinerama1_2%3a1.1.4-3build1_amd64.deb ... 124s Unpacking libxinerama1:amd64 (2:1.1.4-3build1) ... 124s Selecting previously unselected package libxrandr2:amd64. 124s Preparing to unpack .../091-libxrandr2_2%3a1.5.4-1_amd64.deb ... 124s Unpacking libxrandr2:amd64 (2:1.5.4-1) ... 124s Selecting previously unselected package libgles2:amd64. 124s Preparing to unpack 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unselected package libmaeparser1:amd64. 125s Preparing to unpack .../107-libmaeparser1_1.3.1-1build3_amd64.deb ... 125s Unpacking libmaeparser1:amd64 (1.3.1-1build3) ... 125s Selecting previously unselected package librdkit1t64. 125s Preparing to unpack .../108-librdkit1t64_202503.1-4_amd64.deb ... 125s Unpacking librdkit1t64 (202503.1-4) ... 125s Selecting previously unselected package python3-rdkit. 125s Preparing to unpack .../109-python3-rdkit_202503.1-4_amd64.deb ... 125s Unpacking python3-rdkit (202503.1-4) ... 125s Selecting previously unselected package refmac-dictionary. 125s Preparing to unpack .../110-refmac-dictionary_5.41-3_all.deb ... 125s Unpacking refmac-dictionary (5.41-3) ... 126s Selecting previously unselected package libasound2-data. 126s Preparing to unpack .../111-libasound2-data_1.2.14-1ubuntu1_all.deb ... 126s Unpacking libasound2-data (1.2.14-1ubuntu1) ... 126s Selecting previously unselected package libasound2t64:amd64. 126s Preparing to unpack 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to unpack .../117-libmmdb2-0_2.0.22-1_amd64.deb ... 126s Unpacking libmmdb2-0:amd64 (2.0.22-1) ... 126s Selecting previously unselected package libevent-core-2.1-7t64:amd64. 126s Preparing to unpack .../118-libevent-core-2.1-7t64_2.1.12-stable-10build1_amd64.deb ... 126s Unpacking libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 126s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 126s Preparing to unpack .../119-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_amd64.deb ... 126s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 126s Selecting previously unselected package libpsm2-2. 126s Preparing to unpack .../120-libpsm2-2_11.2.185-2.1_amd64.deb ... 126s Unpacking libpsm2-2 (11.2.185-2.1) ... 126s Selecting previously unselected package librdmacm1t64:amd64. 126s Preparing to unpack .../121-librdmacm1t64_56.1-1ubuntu1_amd64.deb ... 126s Unpacking librdmacm1t64:amd64 (56.1-1ubuntu1) ... 126s Selecting previously unselected package libfabric1:amd64. 126s Preparing to unpack .../122-libfabric1_2.1.0-1.1_amd64.deb ... 126s Unpacking libfabric1:amd64 (2.1.0-1.1) ... 126s Selecting previously unselected package libhwloc15:amd64. 126s Preparing to unpack .../123-libhwloc15_2.12.2-1_amd64.deb ... 126s Unpacking libhwloc15:amd64 (2.12.2-1) ... 126s Selecting previously unselected package libllvm17t64:amd64. 126s Preparing to unpack .../124-libllvm17t64_1%3a17.0.6-22build1_amd64.deb ... 126s Unpacking libllvm17t64:amd64 (1:17.0.6-22build1) ... 127s Selecting previously unselected package libamd-comgr2:amd64. 127s Preparing to unpack .../125-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build3_amd64.deb ... 127s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build3) ... 127s Selecting previously unselected package libhsakmt1:amd64. 127s Preparing to unpack .../126-libhsakmt1_6.2.4+ds-1_amd64.deb ... 127s Unpacking libhsakmt1:amd64 (6.2.4+ds-1) ... 127s Selecting previously unselected package 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(1.1.15+dfsg-1build1) ... 132s Setting up libcootapi-dev (1.1.15+dfsg-1build1) ... 132s Processing triggers for libc-bin (2.42-0ubuntu3) ... 132s Processing triggers for man-db (2.13.1-1) ... 133s Processing triggers for libglib2.0-0t64:amd64 (2.86.0-2) ... 133s Setting up libgtk-4-1:amd64 (4.20.1+ds-2) ... 133s Setting up gir1.2-gtk-4.0:amd64 (4.20.1+ds-2) ... 133s Setting up coot (1.1.15+dfsg-1build1) ... 133s Processing triggers for libc-bin (2.42-0ubuntu3) ... 135s autopkgtest [17:36:03]: test command1: coot --self-test 135s autopkgtest [17:36:03]: test command1: [----------------------- 135s INFO:: Running internal self tests 140s INFO:: Test Clipper core : OK 140s INFO:: Test Clipper contrib: OK 140s run_internal_tests() --------- we have 8 internal test functionns 140s Entering test: kevin's torsion test 140s PASS: kevin's torsion test 140s Entering test: test_alt_conf_rotamers 140s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 140s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 140s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 140s chis.size() 2 (should be 2) 140s DEBUG:: i_rot 0 chi: alt-conf: A chi-1: 65.911 140s DEBUG:: i_rot 1 chi: alt-conf: B chi-1: -144.68 140s For residue 80 chis size 1 140s residue 80 chis: -56.8781 -80.8484 140s PASS: test_alt_conf_rotamers 140s Entering test: test_fragmemt_atom_selection 140s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 140s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 140s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 140s ----------------- create_mmdbmanager_from_inverted_atom_selection() 140s n_initial: 1465 n_1: 1401 n_2: 64 140s PASS: test_fragmemt_atom_selection 140s Entering test: test_add_atom 140s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 140s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 140s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 140s PASS: test_add_atom 140s Entering test: test segid exchange 140s DEBUG:: get_atom_selection() with file "/usr/share/coot/data/tutorial-modern.pdb" use_gemmi: 0 140s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 140s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 140s Test with a rogue segid 140s INFO:: No consistent segids for residue 1 140s PASS: test segid exchange 140s Entering test: test peak search non-close 140s mtz_file_name /usr/share/coot/data/rnasa-1.8-all_refmac1.mtz 140s FFT Reso...0.444444 140s Sampling rate...1.5 140s Grid...Nuvw = ( 132, 160, 80) 140s Cell... Cell (64.897,78.323,38.792, 90, 90, 90) 140s Spacegroup...P 21 21 21 140s There are 2260 peaks and 0 problem peaks 140s PASS: test peak search non-close 140s Entering test: test symop card 140s 1 0 0 140s 0 1 0 140s 0 0 1 140s translations: -1 0 0 140s PASS: test symop card 140s Entering test: SSM sequence alignment output 140s 140s -- 140s Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG 140s Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 140s 140s Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC 140s 140s -- 140s Moving: D 140s Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 140s 140s -- 140s Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG 140s Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG 140s 140s -- 140s PASS: SSM sequence alignment output 140s autopkgtest [17:36:08]: test command1: -----------------------] 140s autopkgtest [17:36:08]: test command1: - - - - - - - - - - results - - - - - - - - - - 140s command1 PASS 141s autopkgtest [17:36:09]: test command2: preparing testbed 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s Solving dependencies... 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s autopkgtest [17:36:11]: test command2: pyrogen --help 143s autopkgtest [17:36:11]: test command2: [----------------------- 143s Usage: pyrogen [options] file-or-SMILES 143s if file-or-SMILES has extension ".smi" or ".smiles" then it is treated as a file 143s 143s Options: 143s -h, --help show this help message and exit 143s -c FILE, --mmcif=FILE 143s Make restraints from input mmcif FILE 143s -m FILE, --mol=FILE Make restraints from input sdf/mol FILE 143s -r COMP_ID, --residue-type=COMP_ID 143s Create restraints for this type. Default is LIG 143s -4, --quartet-planes Use 4-atom plane restraints, 143s forces --quartet-hydrogens 143s -H, --quartet-hydrogens 143s Use 4-atom hydrogen plane restraints 143s -b, --no-shift-hydrogen-atoms 143s Stop addition or deletion of Hydrogen atoms for 143s formally-charged atoms 143s -n, --no-mogul Don't run CSD Mogul to update bond and angle 143s restraints 143s -N COMPOUND_NAME, --name=COMPOUND_NAME 143s Compound name 143s -S, --smiles Write the SMILES for the input molecule 143s -t, --tautomers Show SMILES for tautomers, don't generate restraints 143s -T MOGUL_DIR, --tmp-directory=MOGUL_DIR 143s Directory into which the tmp files (e.g. for mogul) 143s are written 143s -d OUTPUT_DIR, --directory=OUTPUT_DIR 143s Directory into which the output files (e.g. mmCIF and 143s PDB) are written 143s -o OUTPUT_POSTFIX, --output-postfix=OUTPUT_POSTFIX 143s string to add to output file names, default is 143s "pyrogen" 143s -p, --picture Additionally output a chemical diagram PNG 143s -P, --preserve-input-coordinates 143s Preserve the inputput coordinates (if possible) 143s -v, --version Print version information 143s -a, --no-match-vs-reference-dictionaries 143s Don't match atom names vs. dictionary molecules 143s (default False) 143s -R DICT_FILES_FOR_NAMES_MATCH, --reference-dictionary-files=DICT_FILES_FOR_NAMES_MATCH 143s Try to match the atom names of the output molecule to 143s this dictionary in these files (comma-separated list) 143s -C COMP_ID_LIST_FOR_NAMES_MATCH, --reference-dictionary-comp-ids=COMP_ID_LIST_FOR_NAMES_MATCH 143s Try to match the atom names of the output molecule to 143s these comp-ids (comma-separated list) 143s -w, --wwPDB Fetch the wwPDB ligand definition and use that 143s -f FETCH (Just) fetch from the PDBe the CCD entry for the given 143s compound-id 143s -q, --quiet print less messages 144s autopkgtest [17:36:12]: test command2: -----------------------] 144s command2 PASS 144s autopkgtest [17:36:12]: test command2: - - - - - - - - - - results - - - - - - - - - - 145s autopkgtest [17:36:13]: @@@@@@@@@@@@@@@@@@@@ summary 145s command1 PASS 145s command2 PASS